id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14882 Bundle ChimeraX-NMRSTAR has no module chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-12.7.2-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/cottiers/Desktop/Pry1-040424.cxs Log from Tue Apr 2 17:20:03 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/cottiers/Desktop/pry1b.cxs format session Log from Thu Mar 7 17:37:50 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Volumes/CottierS/My > Documents/2024-0301/prys/bioinformatic/Pry1-consurf.cxs"" Log from Thu Mar 7 16:41:11 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5jys format mmcif fromDatabase pdb 5jys title: Pry1 CAP domain [more info...] Chain information for 5jys #1 --- Chain | Description | UniProt A | Protein PRY1 | PRY1_YEAST Non-standard residues in 5jys #1 --- MG — magnesium ion > open /Users/stribnyj/Downloads/5JYSA_with_Conservation_Scores.cif mmCIF parsing error: PDBx/mmCIF styling lost near line 2302 > ui tool show ""AlphaFold Error Plot"" Must choose path to predicted aligned file > set bgColor white > close > open P47032 fromDatabase alphafold Summary of feedback from opening P47032 fetched from alphafold --- notes | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Fetching compressed AlphaFold P47032 from https://alphafold.ebi.ac.uk/files/AF-P47032-F1-model_v4.cif Chain information for AlphaFold P47032 #1 --- Chain | Description | UniProt A | Protein PRY1 | PRY1_YEAST > save /Users/stribnyj/Desktop/PryAF.pdb relModel #1 > color PuOr-10 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color byatom PuOr-10 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select add #1 2155 atoms, 2201 bonds, 299 residues, 1 model selected > color byatom PuOr-10 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword Alignment identifier is 1/A > open /Users/stribnyj/Desktop/PRY1.pdb Summary of feedback from opening /Users/stribnyj/Desktop/PRY1.pdb --- warnings | Ignored bad PDB record found on line 1 SEQRES 1 A 299 MET LYS LEU SER LYS LEU SER ILE LEU THR SER ALA LEU Ignored bad PDB record found on line 2 SEQRES 2 A 299 ALA THR SER ALA LEU ALA ALA PRO ALA VAL VAL THR VAL Ignored bad PDB record found on line 3 SEQRES 3 A 299 THR GLU HIS ALA HIS GLU ALA ALA VAL VAL THR VAL GLN Ignored bad PDB record found on line 4 SEQRES 4 A 299 GLY VAL VAL TYR VAL GLU ASN GLY GLN THR ARG THR THR Ignored bad PDB record found on line 5 SEQRES 5 A 299 TYR GLU THR LEU ALA PRO ALA SER THR ALA THR PRO THR 2195 messages similar to the above omitted > open /Users/stribnyj/PryAF.pdb Chain information for PryAF.pdb #2 --- Chain | Description A | No description available > hide #1 models > show #1 models > close #1 > close > open /Users/stribnyj/PryAF.pdb Chain information for PryAF.pdb #1 --- Chain | Description A | No description available > rainbow > color byattribute bfactor 2155 atoms, 299 residues, atom bfactor range 1 to 9 > ui tool show ""Color Actions"" > ui tool show ""Basic Actions"" > color byattribute bfactor palette cyanmaroon range -1.4,1.4 2155 atoms, 299 residues, atom bfactor range 1 to 9 > color byattribute bfactor palette cyanmaroon range Missing ""range"" keyword's argument > color byattribute bfactor 2155 atoms, 299 residues, atom bfactor range 1 to 9 > show surfaces > color fromatoms atoms > hide surfaces > surface > color fromatoms > color byattribute bfactor palette cyanmaroon range -1.4,1.4 2155 atoms, 299 residues, 1 surfaces, atom bfactor range 1 to 9 > color byattribute bfactor palette cyanmaroon range Missing ""range"" keyword's argument > hide surfaces > color byattribute bfactor 2155 atoms, 299 residues, 1 surfaces, atom bfactor range 1 to 9 > ui tool show ""Color Key"" > ui mousemode right ""color key"" > key blue-white-red :min : :max white: > key blue-white-red :min : :max > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key fontSize 15 > key fontSize 14 > key fontSize 13 > key fontSize 12 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.22000,0.05000 > key size 0.21000,0.05000 > key size 0.20000,0.05000 > key size 0.19000,0.05000 > key size 0.20000,0.05000 > key size 0.20000,0.04000 > key size 0.20000,0.03000 > key size 0.20000,0.02000 > key size 0.20000,0.01000 > key size 0.20000,0.02000 > key pos 0.69000,0.08000 > key pos 0.68000,0.08000 > key pos 0.67000,0.08000 > key pos 0.66000,0.08000 > key pos 0.65000,0.08000 > key pos 0.64000,0.08000 > key pos 0.63000,0.08000 > key pos 0.62000,0.08000 > key pos 0.61000,0.08000 > key pos 0.60000,0.08000 > key pos 0.59000,0.08000 > key pos 0.58000,0.08000 > key pos 0.57000,0.08000 > key pos 0.56000,0.08000 > key pos 0.55000,0.08000 > key pos 0.54000,0.08000 > key pos 0.53000,0.08000 > key pos 0.52000,0.08000 > key pos 0.51000,0.08000 > key pos 0.50000,0.08000 > key pos 0.49000,0.08000 > key pos 0.48000,0.08000 > key pos 0.47000,0.08000 > key pos 0.46000,0.08000 > key pos 0.45000,0.08000 > key tickThickness 5.0 > key tickThickness 6.0 > key tickThickness 7.0 > key tickThickness 8.0 > key tickThickness 9.0 > key tickThickness 10.0 > key tickThickness 9.0 > key tickThickness 8.0 > key tickThickness 7.0 > key tickThickness 6.0 > key tickThickness 5.0 > key tickThickness 4.0 > key tickThickness 3.0 > key tickThickness 4.0 > key colorTreatment distinct > key colorTreatment blended > ui mousemode right translate > ui tool show ""Color Key"" > ui mousemode right ""color key"" > key cyan-white-maroon :min : :max > key blue-white-red :min : :max > color bfactor 2155 atoms, 299 residues, 1 surfaces, atom bfactor range 1 to 9 > show surfaces > hide surfaces > lighting gentle > graphics silhouettes true > show surfaces > hide surfaces > show atoms > hide atoms > select add #2 1 model selected > hide #2 models > show #2 models > select subtract #2 Nothing selected > color bfactor palette cyanmaroon range 0,10 2155 atoms, 299 residues, 1 surfaces, atom bfactor range 1 to 9 > color bfactor palette cyanmaroon range 1,9 2155 atoms, 299 residues, 1 surfaces, atom bfactor range 1 to 9 > ui tool show ""Color Key"" > key cyan-white-maroon :min : :max > ui mousemode right translate > save /Users/stribnyj/Desktop/Pry1-consurf.cxs ——— End of log from Thu Mar 7 16:41:11 2024 ——— opened ChimeraX session > ui mousemode right select > select /A:51 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select /A:251 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel surfaces > select up 48 atoms, 49 bonds, 6 residues, 1 model selected > select up 2155 atoms, 2201 bonds, 299 residues, 2 models selected > show sel surfaces > hide sel surfaces [Repeated 1 time(s)] > select clear > select /A:249 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > save /Users/cottiers/Desktop/pry1b.cxs ——— End of log from Thu Mar 7 17:37:50 2024 ——— opened ChimeraX session Alignment identifier is 1/A > select /A:94 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:93-94 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:93 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:93 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!1 & sel) magenta > show sel atoms > select > /A:57-58,156-158,161-174,181-183,187-198,223-236,249-254,291-294,296-297 462 atoms, 467 bonds, 60 residues, 1 model selected > select /A:233-234 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:233-234 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:234 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:234 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:24 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > select /A:30 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:30 5 atoms, 4 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > select /A:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:44 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > select /A:2 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:2 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!1 & sel) yellow > select /A:4 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:4-6 23 atoms, 22 bonds, 3 residues, 1 model selected > color (#!1 & sel) yellow > save /Users/cottiers/Desktop/Pry1-040424.cxs ——— End of log from Tue Apr 2 17:20:03 2024 ——— opened ChimeraX session > open 5jys Cannot open '5jys': [Errno 1] Operation not permitted: '/Users/cottiers/Downloads/ChimeraX/PDB/5jys.cif' > close session > open 5jys Cannot open '5jys': [Errno 1] Operation not permitted: '/Users/cottiers/Downloads/ChimeraX/PDB/5jys.cif' > open 5jys from pdb_nmr format nmrstar Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/dialog.py"", line 197, in fetch run(self.session, cmd) File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 83, in cmd_open provider_args = mgr.fetch_args(fetches[0][1], format_name=fetches[0][2]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/manager.py"", line 191, in fetch_args args.update(provider_info.bundle_info.run_provider(self.session, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 396, in run_provider api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Bundle %s has no module"" % self.name) chimerax.core.toolshed.ToolshedError: Bundle ChimeraX-NMRSTAR has no module chimerax.core.toolshed.ToolshedError: Bundle ChimeraX-NMRSTAR has no module File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Bundle %s has no module"" % self.name) See log for complete Python traceback. OpenGL version: 4.1 INTEL-18.8.6 OpenGL renderer: Intel Iris OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Macmini7,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 481.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.24f32 Software: System Software Overview: System Version: macOS 12.7.2 (21G1974) Kernel Version: Darwin 21.6.0 Time since boot: 1 day 1:47 Graphics/Displays: Intel Iris: Chipset Model: Intel Iris Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0a2e Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: DELL P2210H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: T735R02814TL Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect assigned normal Tool Shed Tom Goddard Eric Pettersen all ChimeraX